Sequence
atgc intronic sequence ATGC exonic sequencegttgatcctattacatattttctatctcaaattagaattgttttccattggctttagagcacctctatttctttcatgaacccattttcatcaagaattcttactggagctccttggacagtgcagGGTTATCGTGTTCTTGTTGTAGAGCAAACAGAAACACCTGAGCAGCTTGAGCTTCGTCGCAAAGAGAAGGGTTCTAAGGACAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0005g01370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os09g24220.1 (Oryza sativa), 3'ss of exon 6
gttgatcctattacatattttctatctcaaattagaattgttttccattggctttagagcacctctatttctttcatgaacccattttcatcaagaattc-ttactggagctccttggacagtgcagGGTTATCGTGTTCTTGTTGTAGAGCAAACAGAAACACCTGAGCAGCTTGAGCTTCGTCGCAAAGAGAAGGGTTCTAAGGACAAG
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-----------------------------------------gtcagatcatgtttgatatgattttattcttccatggaaaataattacatttttaataagctaacagagttggttg--catcacagGGTTATCGAGTTCTGGTTATCGAGCAGACTGAAACACCGGAGCAGCTTGACCTCCGCCGTAAAGAAACTGGTGTAAAAGACAAG
upper sequence: Vv07s0005g01370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G421541_T02 (Zea mays), 3'ss of exon 6
gttgatcctattacatattttctatctcaaattagaattgttttccattggctttagagcacctctatttctttcatgaacccattttcatcaagaattcttactggagctccttggacagtgcagGGTTATCGTGTTCTTGTTGTAGAGCAAACAGAAACACCTGAGCAGCTTGAGCTTCGTCGCAAAGAGAAGGGTTCTAAGGACAAG
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-------------------------------gtaaacttatttaatgtttttcctca-----ttaaatttcacacataattgcatttt-agcaataacattaattg------------cattacagGGTTATCGAGTTCTGGTTGTCGAGCAAACTGAAACACCTGACCAGCTTGAACTTCGGCGTAAGGAGATGGGTATAAAGGACAAG
upper sequence: Vv07s0005g01370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G40350.1 (Glycine max), 3'ss of exon 6
gttgatcctattacatattttctatctcaaattagaattgttttccattggctt---tagagcacctctatttctttcatgaacccattttcatcaagaatt------cttactggagctccttggacagtgcagGGTTATCGTGTTCTTGTTGTAGAGCAAACAGAAACACCTGAGCAGCTTGAGCTTCGTCGCAAAGAGAAGGGTTCTAAGGACAAG
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gtttgtctcacaaatgactccccccccccccccccccccccctcttttcatctcagatacagactaattacttgtctaacaagccaacctgtaactaggggggaggaacttactaagtttccatggttga-gcagGGTTATCGAGTTCTTGTTGTAGAGCAGACTGATACACCTGAACAGCTGGAGCTTCGTCGCAAGGAGAAGGGCTCTAAAGATAAG
upper sequence: Vv07s0005g01370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S152_6V6.1 (Physcomitrella patens), 3'ss of exon 6
gttgatcctattacatattttctatctcaaattagaattgttttccattggctttagagcacctctatttctttcatgaacccattttcatcaagaattcttactggagctccttggacagtgcagGGTTATCGTGTTCTTGTTGTAGAGCAAACAGAAACACCTGAGCAGCTTGAGCTTCGTCGCAAAGAGAAGGGTTCTAAGGACAAG
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----------------------ttactaatgtttggcgcatct-ctacaagcctc-gagtcttggactgtacctggttggctcaatcctagtatacttctgtaatttaaatcttc--atgttgcagGGATATCGAGTTCTTGTTGTGGAGCAGACAGAGACACCTGATCAGCTGGAAAAACGACGGAAAGAAACTGGTTCAAAGGATAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcatgaacccattttcatcaagaattcttactggagctccttggacagtgcagGGTTATCGTGTTCTTGTTGTAGAGCAAACAGAAACACCTGAGCAGCTTGAGCTTCGTCGCAAAGAGAAGGGTTCTAAGGACAAG
ttcttac putative branch site (score: 2)
attttcat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgatcctattacatattttctatctcaaattagaattgttttccattggctttagagcacctctatttctttcatgaacccattttcatcaagaattcttactggagctccttggacagtgcagGGTTATCGTGTTCTTGTTGTAGAGCAAACAGAAACACCTGAGCAGCTTGAGCTTCGTCGCAAAGAGAAGGGTTCTAAGGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA